def read_cohp(self, ):
"""read COHP anlysis results
"""
from ase.calculators.vasp import VaspDos
dos = VaspDos(os.path.join(self.directory, 'DOSCAR.lobster'))
self.dos = dos._total_dos[1]
self.dos_energies = dos._total_dos[0]
# read COHP results
datas = np.genfromtxt(os.path.join(self.directory, 'COHPCAR.lobster'),
skip_header=3 + len(self.indexs))
self.cohp = datas[:, 1]
self.cohp_energies = datas[:, 0]
# read COOP results
datas = np.genfromtxt(os.path.join(self.directory, 'COOPCAR.lobster'),
skip_header=3 + len(self.indexs))
self.coop = datas[:, 1]
self.coop_energies = datas[:, 0]
# read COBI results
datas = np.genfromtxt(os.path.join(self.directory, 'COBICAR.lobster'),
skip_header=3 + len(self.indexs))
self.cobi = datas[:, 1]
self.cobi_energies = datas[:, 0]
def plot_dos(
cl1,
cl2=None,
dostype=None,
iatom=None,
iatom2=None,
orbitals=('s'),
up=None,
neighbors=6,
show=1,
labels=None,
path='dos',
xlim=(None, None),
ylim=(None, None),
savefile=True,
plot_param={},
suf2='',
fontsize=8,
nsmooth=12,
lts2='--',
split_type='octa',
plot_spin_pol=1,
show_gravity=None,
):
"""
cl1 (CalculationVasp) - object created by add_loop()
dostype (str) - control which dos to plot:
'total' - plot total dos
'diff_total' - difference of total dos, use cl2 for second calculation
'partial' - partial dos
orbitals (list of str) -
any from 's, p, d, py, pz, px, dxy, dyz, dz2, dxz, dx2' where 'p' and 'd' are sums of projections
also to sum around neigbours use p6 and d6 and neighbors parameter
up - 'up2' allows to download the file once again
labels - two manual labels for cl1 and cl2 instead of auto
iatom (int) - number of atom starting from 1 to plot DOS;
iatom ([float]*3) - cartesian coordinates of point around which atoms will be found
show (bool) - whether to show the dos
path (str) - path to folder with images
neighbors - number of neighbours around iatom to plot dos on them using p6 or d6; only p6 is implemented to the moment in plot section
xlim, ylim (tuple)- limits for plot
plot_param - dict of parameters to fit_and_plot
dashes - control of dahsed lines
suf2 - additional suffix
# nsmooth = 15 # smooth of dos
lts2 - style of lines for cl2
split_type -
octa - the names are t2g and eg
tetra - the names are t2 and e
plot_spin_pol -
0 - spin-polarized components are summed up
show_gravity (list) - print gravity centers (i, type, range, ); i - 1 or 2 cl
type (str)
'p6' - for p orbitals of neighbors
'p'
#0 s 1 py 2 pz 3 px 4 dxy 5 dyz 6 dz2 7 dxz 8 dx2
#In all cases, the units of the l- and site projected DOS are states/atom/energy.
"""
if fontsize:
header.mpl.rcParams.update({'font.size': fontsize + 4})
header.mpl.rc('legend', fontsize=fontsize)
if dostype == 'partial':
eld1, eld2 = {}, {}
for i, el in enumerate(cl1.end.get_elements()):
eld1[i + 1] = el
if cl2:
for i, el in enumerate(cl2.end.get_elements()):
eld2[i + 1] = el
if not iatom:
printlog(
'Warning! Please choose atom number *iatom* from the following list:\n'
)
printlog(eld)
sys.exit()
else:
printlog('cl1: Atom',
iatom,
'of type',
eld1[iatom],
'is choosen',
imp='y')
printlog('cl1: Atom numbers:', eld1, imp='y')
printlog('cl1:',
determine_symmetry_positions(cl1.end, eld1[iatom]),
imp='y')
# print(cl2)
if cl2:
if not iatom2:
printlog('Error! provide iatom2!')
printlog('cl2: Atom',
iatom2,
'of type',
eld2[iatom2],
'is choosen',
imp='y')
printlog('cl2:',
determine_symmetry_positions(cl2.end, eld2[iatom2]),
imp='y')
iatom -= 1
if cl2:
if not iatom2:
printlog('Error!, provide *iatom2*!')
iatom2 -= 1
if 'figsize' not in plot_param:
plot_param['figsize'] = (4, 6)
if 'legend' not in plot_param:
plot_param['legend'] = 'best'
"""1. Read dos"""
printlog("------Start plot_dos()-----", imp='Y')
dos = [] # main list for cl1 and cl2
for cl in cl1, cl2:
if cl == None:
continue
if not hasattr(cl, "efermi"):
cl.read_results('o')
printlog(cl.name, 'e_fermi', cl.efermi, imp='Y')
DOSCAR = cl.get_file('DOSCAR', nametype='asoutcar')
printlog('DOSCAR file is ', DOSCAR)
dos.append(VaspDos(DOSCAR, cl.efermi))
#determine number of zero energy
i_efermi = int(
len(dos[0].energy) * -dos[0].energy[0] /
(dos[0].energy[-1] -
dos[0].energy[0])) # number of point with zero fermi energy
if cl2:
i_efermi_e = int(
len(dos[1].energy) * -dos[1].energy[0] /
(dos[1].energy[-1] -
dos[1].energy[0])) # number of point with zero fermi energy
if len(dos[0].dos) == 2:
spin_pol = True
else:
spin_pol = False
"""2. Plot dos for different cases"""
if dostype == 'total':
# print(dos[0].dos)
ylabel = "DOS (states/eV)"
if spin_pol:
dosplot = {
'Tot up': {
'x': dos[0].energy,
'y': smoother(dos[0].dos[0], 10),
'c': 'b',
'ls': '-'
},
'Tot down': {
'x': dos[0].energy,
'y': -smoother(dos[0].dos[1], 10),
'c': 'r',
'ls': '-'
}
}
else:
dosplot = {
'Total': {
'x': dos[0].energy,
'y': smoother(dos[0].dos, 10),
'c': 'b',
'ls': '-'
}
}
# args[nam_down] = {'x':d.energy, 'y':-smoother(d.site_dos(iat, i_orb_down[orb]), nsmooth), 'c':color[orb], 'ls':l, 'label':None}
# xlabel = "Energy (eV)", ylabel = "DOS (states/eV)"
# print(plot_param)
image_name = os.path.join(path, cl1.name + '.dosTotal')
fit_and_plot(show=show,
image_name=image_name,
hor=True,
**plot_param,
**dosplot)
elif dostype == 'diff_total': #no spin-polarized!!!!
ylabel = "DOS (states/eV)"
if len(dos) > 1:
#calculate dos diff
dosd = [(d0 - d1) * e
for d0, d1, e in zip(dos[0].dos, dos[1].dos, dos[0].energy)
] #calculate difference
area = trapz(dosd[:i_efermi], dx=1)
printlog("area under dos difference = ", -area, imp='Y')
fit_and_plot(show=show,
image_name=cl1.name + '--' + cl2.name +
'.dosTotal_Diff',
xlabel="Energy (eV)",
ylabel="DOS (states/eV)",
hor=True,
**plot_param,
Diff_Total=(dos[0].energy, smoother(dosd, 15), 'b-'))
else:
printlog(
'You provided only one calculation; could not use diff_total')
elif 'partial' in dostype:
#Partial dos
#1 p carbon, d Ti
#0 s 1 py 2 pz 3 px 4 dxy 5 dyz 6 dz2 7 dxz 8 dx2
ylabel = "PDOS (states/atom/eV)"
try:
dos[0].site_dos(0, 4)
except:
printlog(
'Error! No information about partial dxy dos in DOSCAR; use LORBIT 12 to calculate it'
)
"""Determine neighbouring atoms """
# printlog("Number of considered neighbors is ", neighbors, imp = 'y')
if type(
iatom
) == int: #for the cases when we need to build surrounding around specific atom in this calculation - just use number of atom
t = cl1.end.typat[iatom]
z = cl1.end.znucl[t - 1]
el = element_name_inv(z)
printlog('Typat of chosen imp atom in cl1 is ', el, imp='y')
surround_center = cl1.end.xcart[iatom]
else: #for the case when coordinates of arbitary point are provided.
surround_center = iatom
el = 'undef'
local_atoms = local_surrounding(surround_center,
cl1.end,
neighbors,
control='atoms',
periodic=True)
numbers = local_atoms[2]
els = cl1.end.get_elements()
el_sur = els[numbers[1]] # element of surrounding type
printlog("Numbers of local atoms:", [n + 1 for n in numbers], imp='Y')
printlog("Elements of local atoms:", [els[i] for i in numbers],
imp='Y')
printlog("List of distances", [round(d, 2) for d in local_atoms[3]],
imp='Y')
iX = numbers[0] # first atom is impurity if exist
# printlog
numbers_list = [numbers] # numbers_list is list of lists
calcs = [cl1]
if cl2:
numbers_list.append([iatom2]) # for cl2 only one atom is supported
calcs.append(cl2)
for cl, d, numbers in zip(calcs, dos, numbers_list):
d.p = [] #central and surrounding
d.d = []
d.p_up = []
d.p_down = []
d.p_down = [] #central and and surrounding
d.d_up = [] #central atom and surrounding atoms
d.d_down = [] #central atom and surrounding atoms
d.t2g_up = []
d.t2g_down = []
d.eg_up = []
d.eg_down = []
d.p_all = [] #sum over all atoms
d.d_all = [] #sum over all atoms
d.p_all_up = [] #sum over all atoms
d.d_all_up = [] #sum over all atoms
d.p_all_down = [] #sum over all atoms
d.d_all_down = [] #sum over all atoms
if 'p_all' in orbitals or 'd_all' in orbitals:
#sum over all atoms
p = []
p_up = []
p_down = []
dd = []
d_up = []
d_down = []
els = cl.end.get_elements()
for i in range(cl.end.natom):
# if 'O' not in els[i]:
# continue
if spin_pol:
plist_up = [d.site_dos(i, l) for l in (2, 4, 6)]
plist_down = [d.site_dos(i, l) for l in (3, 5, 7)]
plist = plist_up + plist_down
p_up.append([sum(x) for x in zip(*plist_up)])
p_down.append([sum(x) for x in zip(*plist_down)])
p.append([sum(x) for x in zip(*plist)])
else:
plist = [d.site_dos(i, l) for l in (1, 2, 3)]
p.append([sum(x) for x in zip(*plist)])
if spin_pol:
dlist_up = [
d.site_dos(i, l) for l in (8, 10, 12, 14, 16)
] #
dlist_down = [
d.site_dos(i, l) for l in (9, 11, 13, 15, 17)
] #
dlist = dlist_up + dlist_down
d_up.append([sum(x) for x in zip(*dlist_up)])
d_down.append([sum(x) for x in zip(*dlist_down)])
dd.append([sum(x) for x in zip(*dlist)])
else:
dlist = [d.site_dos(i, l) for l in (4, 5, 6, 7, 8)] #
dd.append([sum(x) for x in zip(*dlist)])
d.p_all = [sum(pi) for pi in zip(*p)] #sum over all atoms
d.d_all = [sum(di) for di in zip(*dd)]
if spin_pol:
d.p_all_up = [sum(pi) for pi in zip(*p_up)]
d.p_all_down = [sum(pi) for pi in zip(*p_down)]
d.d_all_up = [sum(pi) for pi in zip(*d_up)]
d.d_all_down = [sum(pi) for pi in zip(*d_down)]
#sum by surrounding atoms atoms
n_sur = len(numbers)
for i in numbers: #Now for surrounding atoms in numbers list:
if spin_pol:
plist_up = [d.site_dos(i, l) for l in (2, 4, 6)]
plist_down = [d.site_dos(i, l) for l in (3, 5, 7)]
d.p_up.append([sum(x) for x in zip(*plist_up)])
d.p_down.append([sum(x) for x in zip(*plist_down)])
plist = plist_up + plist_down
d.p.append([sum(x) for x in zip(*plist)])
else:
plist = [d.site_dos(i, l) for l in (1, 2, 3)]
d.p.append([sum(x) for x in zip(*plist)])
if spin_pol:
dlist_up = [d.site_dos(i, l)
for l in (8, 10, 12, 14, 16)] #
dlist_down = [
d.site_dos(i, l) for l in (9, 11, 13, 15, 17)
] #
dlist = dlist_up + dlist_down
d.d.append([sum(x) for x in zip(*dlist)])
d.d_up.append([sum(x) for x in zip(*dlist_up)])
d.d_down.append([sum(x) for x in zip(*dlist_down)])
t2g_down = [d.site_dos(i, l) for l in (9, 11, 15)]
eg_down = [d.site_dos(i, l) for l in (13, 17)]
t2g_up = [d.site_dos(i, l) for l in (8, 10, 14)]
eg_up = [d.site_dos(i, l) for l in (12, 16)]
d.t2g_down.append([sum(x) for x in zip(*t2g_down)])
d.eg_down.append([sum(x) for x in zip(*eg_down)])
d.t2g_up.append([sum(x) for x in zip(*t2g_up)])
d.eg_up.append([sum(x) for x in zip(*eg_up)])
else:
dlist = [d.site_dos(i, l) for l in (4, 5, 6, 7, 8)] #
d.d.append([sum(x) for x in zip(*dlist)])
d.p6 = [sum(pi) / n_sur for pi in zip(*d.p)
] #sum over neighbouring atoms now only for spin up
if spin_pol:
d.p6_up = [sum(pi) / n_sur for pi in zip(*d.p_up)
] #sum over neighbouring atoms now only for spin up
d.p6_down = [
sum(pi) / n_sur for pi in zip(*d.p_down)
] #sum over neighbouring atoms now only for spin up
d.d6 = [sum(di) for di in zip(*d.d)] #sum over neighbouring atoms
"""Plotting"""
# nsmooth = 15 # smooth of dos
d1 = dos[0]
ds = [d1]
names = []
names = [cl1.id[0] + '_at_' + eld1[iatom + 1] + str(iatom + 1)]
atoms = [iatom]
els = [eld1[iatom + 1]]
lts = [
'-',
] #linetypes
if cl2:
ds.append(dos[1])
d2 = dos[1]
# if labels:
# names.append(labels[1])
# else:
names.append(cl2.id[0] + '_at_' + eld2[iatom2 + 1] +
str(iatom2 + 1))
lts.append(lts2)
atoms.append(iatom2)
els.append(eld2[iatom2 + 1])
if not spin_pol:
plot_spin_pol = 0 # could not plot spin polarization for non-spin polarization plot
if 'dashes' in plot_param:
dashes = plot_param['dashes']
del plot_param['dashes']
else:
dashes = (5, 1)
energy1 = dos[0].energy
args = {}
if spin_pol:
i_orb = {
's': 0,
'py': 2,
'pz': 4,
'px': 6,
'dxy': 8,
'dyz': 10,
'dz2': 12,
'dxz': 14,
'dx2': 16
}
i_orb_down = {
's': 1,
'py': 3,
'pz': 5,
'px': 7,
'dxy': 9,
'dyz': 11,
'dz2': 13,
'dxz': 15,
'dx2': 17
}
else:
i_orb = {
's': 0,
'py': 1,
'pz': 2,
'px': 3,
'dxy': 4,
'dyz': 5,
'dz2': 6,
'dxz': 7,
'dx2': 8
}
# color = {'s':'k', 'p':'#F14343', 'd':'#289191', 'py':'g', 'pz':'b', 'px':'c', 'dxy':'m', 'dyz':'c', 'dz2':'k', 'dxz':'r', 'dx2':'g', 't2g':'b', 'eg':'g', 'p6':'k'}
color = {
's': 'k',
'p': '#FF0018',
'd': '#138BFF',
'py': 'g',
'pz': 'b',
'px': 'c',
'dxy': 'm',
'dyz': 'c',
'dz2': 'k',
'dxz': 'r',
'dx2': 'g',
't2g': '#138BFF',
'eg': '#8E12FF',
'p6': '#FF0018',
'p_all': 'r',
'd_all': 'b'
} #http://paletton.com/#uid=54-100kwi++bu++hX++++rd++kX
# color = {'s':'k', 'p':'r', 'd':'g', 'py':'g', 'pz':'b', 'px':'c', 'dxy':'m', 'dyz':'c', 'dz2':'m', 'dxz':'r', 'dx2':'g'}
for orb in orbitals:
i = 0
for n, l, iat, el, d in zip(names, lts, atoms, els, ds):
if el in ['Fe', 'Co', 'V', 'Mn'] and orb in ['p', 's']:
continue
if el == 'O' and orb in ('d', 't2g', 'eg', 'dxy', 'dyz', 'dxz',
'dz2', 'dx2'):
continue
nam = orb
nam_down = nam + '_down'
# print('name', n)
# print('lts', l)
if labels:
formula = labels[i]
else:
formula = latex_chem(n.split('.')[0])
i += 1
if spin_pol:
nam += ''
suf = '; ' + n
nam += suf
nam_down += suf
if orb == 'p':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.p_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb,
'dashes': dashes
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.p_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None,
'dashes': dashes
}
color[orb] = 'c'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.p[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb,
'dashes': dashes
}
elif orb == 'p6':
# now spin-polarized components could not be shown
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.p6_up, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el_sur + suf2 + ' p',
'dashes': dashes
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.p6_down, nsmooth),
'c': color[orb],
'ls': l,
'label': None,
'dashes': dashes
}
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.p6, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el_sur + suf2 + ' p',
'dashes': dashes
}
elif orb == 'd':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.d_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.d_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
color[orb] = 'm'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.d[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
elif orb == 't2g':
if split_type == 'octa':
orb_name = orb
elif split_type == 'tetra':
orb_name = 't2'
args[nam] = {
'x': d.energy,
'y': smoother(d.t2g_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb_name
}
if spin_pol:
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.t2g_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
elif orb == 'eg':
if split_type == 'octa':
orb_name = orb
elif split_type == 'tetra':
orb_name = 'e'
args[nam] = {
'x': d.energy,
'y': smoother(d.eg_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb_name
}
if spin_pol:
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.eg_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
elif orb == 'p_all':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.p_all_up, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.p_all_down, nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
# color[orb] = 'm'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.p_all, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
elif orb == 'd_all':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.d_all_up, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.d_all_down, nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
# color[orb] = 'm'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.d_all, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
else:
# args[nam] = (d.energy, smoother(d.site_dos(iat, i_orb[orb]), nsmooth), color[orb]+l)
args[nam] = {
'x': d.energy,
'y': smoother(d.site_dos(iat, i_orb[orb]), nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
if spin_pol:
args[nam_down] = {
'x':
d.energy,
'y':
-smoother(d.site_dos(iat, i_orb_down[orb]),
nsmooth),
'c':
color[orb],
'ls':
l,
'label':
None
}
# args[nam_down] = (d.energy, -smoother(d.site_dos(iat, i_orb_down[orb]), nsmooth), color[orb]+l)
"""Additional dos analysis; to be refined"""
if show_gravity:
if show_gravity[0] == 1:
d = d1
elif show_gravity[0] == 2:
d = d2
if show_gravity[2]:
erange = show_gravity[2]
else:
erange = (-100, 0)
if show_gravity[1] == 'p6':
gc = det_gravity2(d.energy, d.p6, erange)
printlog(
'Gravity center for cl1 for p6 for {:} is {:5.2f}'.format(
erange, gc),
imp='Y')
# gc = det_gravity2(d.energy, d.d[0], erange)
# printlog('Gravity center for cl1 for d for {:} is {:5.2f}'.format(erange, gc), imp = 'Y')
elif show_gravity[1] == 'p':
gc = det_gravity2(d.energy, d.p[0],
erange) # for first atom for cl2
elif show_gravity[1] == 'p_all':
gc = det_gravity2(d.energy, d.p_all,
erange) # for first atom for cl2
printlog('Gravity center for cl1 for p_all for {:} is {:5.2f}'.
format(erange, gc),
imp='Y')
plot_param['ver_lines'] = [{'x': gc, 'c': 'k', 'ls': '--'}]
"""Plot everything"""
image_name = os.path.join(
path, '_'.join(names) + '.' + ''.join(orbitals) + '.' + el +
str(iat + 1))
if 'xlabel' not in plot_param:
plot_param['xlabel'] = "Energy (eV)"
if 'ylabel' not in plot_param:
plot_param['ylabel'] = ylabel
fit_and_plot(
show=show,
image_name=image_name,
hor=True,
# title = cl1.name.split('.')[0]+'; V='+str(round(cl1.vol) )+' $\AA^3$; Impurity: '+el,
**plot_param,
**args)
# printlog("Writing file", image_name, imp = 'Y')
if 0:
"""Calculate d DOS at Fermi level"""
nn = 50 #number to integrate in both directions
x1 = dos[0].energy[i_efermi - nn:i_efermi + nn]
y1 = smoother(dos[0].d6, nsmooth)[i_efermi - nn:i_efermi + nn]
x2 = dos[1].energy[i_efermi_e - nn:i_efermi_e + nn]
y2 = smoother(dos[1].d6, nsmooth)[i_efermi_e - nn:i_efermi_e + nn]
f1 = interp1d(x1, y1, kind='cubic')
f2 = interp1d(x2, y2, kind='cubic')
# if debug: print '\n'
# if debug: print dos[0].d6[i_efermi] - dos[1].d6[i_efermi_e], " - by points; change of d Ti DOS at the Fermi level due to the carbon"
# if debug: print f2(0), f1(0)
e_at_Ef_shift = f1(0) - f2(0)
printlog(
"{:5.2f} reduction of d dos at Fermi level; smoothed and interpolated"
.format(e_at_Ef_shift),
imp='Y')
if 0:
"""Calculate second derivative of d at the Fermi level"""
# tck1 = interpolate.splrep(x1, y1, s=0)
# tck2 = interpolate.splrep(x2, y2, s=0)
# e_at_Ef_shift_spline = interpolate.splev(0, tck1, der=0) - interpolate.splev(0, tck2, der=0)
# if debug: print "{:5.2f} smoothed and interpolated from spline".format( e_at_Ef_shift_spline )
# # if debug: print type(interpolate.splev(0, tck1, der=2))
# if debug: print "{:5.2f} {:5.2f} gb and bulk second derivative at Fermi from spline".format( float(interpolate.splev(0, tck1, der=2)), float(interpolate.splev(0, tck2, der=2)) )
if 0:
"""Calculate shift of d orbitals after adding impurity"""
d_shift = det_gravity(dos[0], Erange=(-2.8, 0)) - det_gravity(
dos[1], Erange=(-2.8, 0)
) #negative means impurity shifts states to negative energies, which is favourable
printlog("{:5.2f} Shift of Ti d center of gravity".format(d_shift),
imp='Y')
# if debug: print det_gravity(dos[0], Erange = (-2.8, 0)), det_gravity(dos[1], Erange = (-2.8, 0))
"""Calculate correlation between imp p and matrix d"""
def rmsdiff(a, b):
# rms difference of vectors a and b:
#Root-mean-square deviation
rmsdiff = 0
for (x, y) in zip(a, b):
rmsdiff += (
x -
y)**2 # NOTE: overflow danger if the vectors are long!
return math.sqrt(rmsdiff / min(len(a), len(b)))
pd_drms = 1 / rmsdiff(
dos[0].p,
dos[0].d6) # the higher the number the higher hybridization
printlog("{:5.2f} p-d hybridization estimate".format(pd_drms),
imp='Y')
# if debug: print "sqeuclidean", sqeuclidean(dos[0].p, dos[0].d6)/len(dos[0].d6)
# if debug: print "pearsonr", pearsonr(dos[0].p, dos[0].d6) #Pearson correlation coefficient; only shape; the larger number means more similarity in shape
# def autocorr(x):
# result = np.correlate(x, x, mode='full')
# return result[result.size/2:]
printlog("------End plot_dos()-----\n\n")
return {'name': cl1.name, 'filename': image_name}
from step0 import *
from numpy import *
from ase.dft import DOS
from ase.dft import get_distribution_moment
from ase.calculators.vasp import VaspDos
os.chdir('work-dos')
emax, emin, ngrid, efermi = dos_info('DOSCAR')
vdos = VaspDos()
vdos.read_doscar('DOSCAR')
vdos._set_efermi(efermi)
e = vdos.energy
dos_up = vdos.dos[0]
dos_down = vdos.dos[1]
dos_total = dos_up + dos_down
dos_s_up = np.zeros(len(e))
dos_p_up = np.zeros(len(e))
dos_d_up = np.zeros(len(e))
dos_s_down = np.zeros(len(e))
dos_p_down = np.zeros(len(e))
dos_d_down = np.zeros(len(e))
for i in range(len(atoms)):
dos_s_up += vdos.site_dos(i, 's-up')
dos_p_up += vdos.site_dos(i, 'px-up') + vdos.site_dos(
b = a / 2.
bulk = Atoms([Atom('Pd', (0.0, 0.0, 0.0))],
cell=[(0, b, b),
(b, 0, b),
(b, b, 0)])
with jasp('bulk/pd-ados',
encut=300,
xc='PBE',
lreal=False,
rwigs=[1.5], # wigner-seitz radii for ados
kpts=(8, 8, 8),
atoms=bulk) as calc:
# this runs the calculation
bulk.get_potential_energy()
# now get results
ados = VaspDos(efermi=calc.get_fermi_level())
energies = ados.energy # energy is an attribute, not a function
dos = ados.site_dos(0, 'd') # this is a function, get d-orbitals on atom 0
# we will select energies in the range of -10, 5
ind = (energies < 5) & (energies > -10)
energies = energies[ind]
dos = dos[ind]
Nstates = np.trapz(dos, energies)
occupied = energies <= 0.0
N_occupied_states = np.trapz(dos[occupied], energies[occupied])
# first moment
ed = np.trapz(energies * dos, energies) / Nstates
# second moment
wd2 = np.trapz(energies**2 * dos, energies) / Nstates
print 'Total # states = {0:1.2f}'.format(Nstates)
print 'number of occupied states = {0:1.2f}'.format(N_occupied_states)
a = 3.9 # approximate lattice constant
b = a / 2.
bulk = Atoms([Atom('Pd', (0.0, 0.0, 0.0))],
cell=[(0, b, b), (b, 0, b), (b, b, 0)])
with jasp(
'bulk/pd-ados',
encut=300,
xc='PBE',
lreal=False,
rwigs=[1.5], # wigner-seitz radii for ados
kpts=(8, 8, 8),
atoms=bulk) as calc:
# this runs the calculation
bulk.get_potential_energy()
# now get results
ados = VaspDos(efermi=calc.get_fermi_level())
energies = ados.energy # energy is an attribute, not a function
dos = ados.site_dos(0, 'd') # this is a function, get d-orbitals on atom 0
# we will select energies in the range of -10, 5
ind = (energies < 5) & (energies > -10)
energies = energies[ind]
dos = dos[ind]
Nstates = np.trapz(dos, energies)
occupied = energies <= 0.0
N_occupied_states = np.trapz(dos[occupied], energies[occupied])
# first moment
ed = np.trapz(energies * dos, energies) / Nstates
# second moment
wd2 = np.trapz(energies**2 * dos, energies) / Nstates
print 'Total # states = {0:1.2f}'.format(Nstates)
print 'number of occupied states = {0:1.2f}'.format(N_occupied_states)
def calc_to_dict(calc, **kwargs):
d = {'doc': '''JSON representation of a VASP calculation.
energy is in eV
forces are in eV/\AA
stress is in GPa (sxx, syy, szz, syz, sxz, sxy)
magnetic moments are in Bohr-magneton
The density of states is reported with E_f at 0 eV.
Volume is reported in \AA^3
Coordinates and cell parameters are reported in \AA
If atom-projected dos are included they are in the form:
{ados:{energy:data, {atom index: {orbital : dos}}}
'''}
d['incar'] = {'doc': 'INCAR parameters'}
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.float_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.exp_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.string_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.int_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.bool_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.list_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.dict_params.items())))
d['input'] = calc.input_params
d['potcar'] = calc.get_pseudopotentials()
d['atoms'] = atoms_to_dict(calc.get_atoms())
d['data'] = {'doc': 'Data from the output of the calculation'}
atoms = calc.get_atoms()
d['data']['total_energy'] = atoms.get_potential_energy()
d['data']['forces'] = atoms.get_forces().tolist()
# There are times when no stress is calculated
try:
stress = atoms.get_stress()
except NotImplementedError:
stress = None
except AssertionError:
stress = None
if stress is not None:
d['data']['stress'] = atoms.get_stress().tolist()
else:
d['data']['stress'] = None
d['data']['fermi_level'] = calc.get_fermi_level()
d['data']['volume'] = atoms.get_volume()
if calc.spinpol:
d['data']['magmom'] = atoms.get_magnetic_moment()
if (calc.int_params.get('lorbit', 0) >= 10
or calc.list_params.get('rwigs', None)):
try:
d['data']['magmoms'] = atoms.get_magnetic_moments().tolist()
except AttributeError:
d['data']['magmoms'] = None
# store the metadata
if hasattr(calc, 'metadata'):
d['metadata'] = calc.metadata
if kwargs.get('dos', None):
from ase.dft.dos import DOS
dos = DOS(calc, width=kwargs.get('width', 0.2))
e = dos.get_energies()
d['data']['dos'] = {'doc': 'Total density of states'}
d['data']['dos']['e'] = e.tolist()
if calc.spinpol:
d['data']['dos']['dos-up'] = dos.get_dos(spin=0).tolist()
d['data']['dos']['dos-down'] = dos.get_dos(spin=1).tolist()
else:
d['data']['dos']['dos'] = dos.get_dos().tolist()
if kwargs.get('ados', None):
from ase.calculators.vasp import VaspDos
ados = VaspDos(efermi=calc.get_fermi_level())
d['data']['ados'] = {'doc': 'Atom projected DOS'}
nonspin_orbitals_no_phase = ['s', 'p', 'd']
nonspin_orbitals_phase = ['s', 'py', 'pz', 'px',
'dxy', 'dyz', 'dz2', 'dxz', 'dx2']
spin_orbitals_no_phase = []
for x in nonspin_orbitals_no_phase:
spin_orbitals_no_phase += ['{0}-up'.format(x)]
spin_orbitals_no_phase += ['{0}-down'.format(x)]
spin_orbitals_phase = []
for x in nonspin_orbitals_phase:
spin_orbitals_phase += ['{0}-up'.format(x)]
spin_orbitals_phase += ['{0}-down'.format(x)]
if calc.spinpol and calc.int_params['lorbit'] != 11:
orbitals = spin_orbitals_no_phase
elif calc.spinpol and calc.int_params['lorbit'] == 11:
orbitals = spin_orbitals_phase
elif calc.int_params['lorbit'] != 11:
orbitals = nonspin_orbitals_no_phase
else:
orbitals = nonspin_orbitals_phase
for i, atom in enumerate(atoms):
d['data']['ados']['energy'] = ados.energy.tolist()
d['data']['ados'][i] = {}
for orbital in orbitals:
d['data']['ados'][i][orbital] = ados.site_dos(0, orbital).tolist()
# convert all numpy arrays to lists
for key in d:
try:
d[key] = d[key].tolist()
except:
pass
for key in d['input']:
try:
d['input'][key] = d['input'][key].tolist()
except:
pass
return d
from step0 import *
from numpy import *
from ase.dft import DOS
from ase.dft import get_distribution_moment
from ase.calculators.vasp import VaspDos
os.chdir('work-dos')
emax, emin, ngrid, efermi = dos_info('DOSCAR')
vdos = VaspDos()
vdos.read_doscar('DOSCAR')
vdos._set_efermi(efermi)
e = vdos.energy
dos_up = vdos.dos[0]
dos_down = vdos.dos[1]
dos_total = dos_up + dos_down
dos_s_up = np.zeros(len(e))
dos_p_up = np.zeros(len(e))
dos_d_up = np.zeros(len(e))
dos_s_down = np.zeros(len(e))
dos_p_down = np.zeros(len(e))
dos_d_down = np.zeros(len(e))
for i in range(len(atoms)):
dos_s_up += vdos.site_dos(i,'s-up')
def calc_to_dict(calc, **kwargs):
"""Convert calc to a dictionary."""
d = {
'doc':
'''JSON representation of a VASP calculation.
energy is in eV
forces are in eV/\AA
stress is in GPa (sxx, syy, szz, syz, sxz, sxy)
magnetic moments are in Bohr-magneton
The density of states is reported with E_f at 0 eV.
Volume is reported in \AA^3
Coordinates and cell parameters are reported in \AA
If atom-projected dos are included they are in the form:
{ados:{energy:data, {atom index: {orbital : dos}}}
'''
}
d['incar'] = {'doc': 'INCAR parameters'}
d['incar'].update(
dict(
filter(lambda item: item[1] is not None,
calc.float_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.exp_params.items())))
d['incar'].update(
dict(
filter(lambda item: item[1] is not None,
calc.string_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.int_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.bool_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.list_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.dict_params.items())))
d['input'] = calc.input_params
d['potcar'] = calc.get_pseudopotentials()
d['atoms'] = atoms_to_dict(calc.get_atoms())
d['data'] = {'doc': 'Data from the output of the calculation'}
atoms = calc.get_atoms()
d['data']['total_energy'] = atoms.get_potential_energy()
d['data']['forces'] = atoms.get_forces().tolist()
# There are times when no stress is calculated
try:
stress = atoms.get_stress()
except NotImplementedError:
stress = None
except AssertionError:
stress = None
if stress is not None:
d['data']['stress'] = atoms.get_stress().tolist()
else:
d['data']['stress'] = None
d['data']['fermi_level'] = calc.get_fermi_level()
d['data']['volume'] = atoms.get_volume()
if calc.spinpol:
d['data']['magmom'] = atoms.get_magnetic_moment()
if (calc.int_params.get('lorbit', 0) >= 10
or calc.list_params.get('rwigs', None)):
try:
d['data']['magmoms'] = atoms.get_magnetic_moments().tolist()
except AttributeError:
d['data']['magmoms'] = None
# store the metadata
if hasattr(calc, 'metadata'):
d['metadata'] = calc.metadata
if kwargs.get('dos', None):
from ase.dft.dos import DOS
dos = DOS(calc, width=kwargs.get('width', 0.2))
e = dos.get_energies()
d['data']['dos'] = {'doc': 'Total density of states'}
d['data']['dos']['e'] = e.tolist()
if calc.spinpol:
d['data']['dos']['dos-up'] = dos.get_dos(spin=0).tolist()
d['data']['dos']['dos-down'] = dos.get_dos(spin=1).tolist()
else:
d['data']['dos']['dos'] = dos.get_dos().tolist()
if kwargs.get('ados', None):
from ase.calculators.vasp import VaspDos
ados = VaspDos(efermi=calc.get_fermi_level())
d['data']['ados'] = {'doc': 'Atom projected DOS'}
nonspin_orbitals_no_phase = ['s', 'p', 'd']
nonspin_orbitals_phase = [
's', 'py', 'pz', 'px', 'dxy', 'dyz', 'dz2', 'dxz', 'dx2'
]
spin_orbitals_no_phase = []
for x in nonspin_orbitals_no_phase:
spin_orbitals_no_phase += ['{0}-up'.format(x)]
spin_orbitals_no_phase += ['{0}-down'.format(x)]
spin_orbitals_phase = []
for x in nonspin_orbitals_phase:
spin_orbitals_phase += ['{0}-up'.format(x)]
spin_orbitals_phase += ['{0}-down'.format(x)]
if calc.spinpol and calc.int_params['lorbit'] != 11:
orbitals = spin_orbitals_no_phase
elif calc.spinpol and calc.int_params['lorbit'] == 11:
orbitals = spin_orbitals_phase
elif calc.int_params['lorbit'] != 11:
orbitals = nonspin_orbitals_no_phase
else:
orbitals = nonspin_orbitals_phase
for i, atom in enumerate(atoms):
d['data']['ados']['energy'] = ados.energy.tolist()
d['data']['ados'][i] = {}
for orbital in orbitals:
d['data']['ados'][i][orbital] = ados.site_dos(
0, orbital).tolist()
# convert all numpy arrays to lists
for key in d:
try:
d[key] = d[key].tolist()
except:
pass
for key in d['input']:
try:
d['input'][key] = d['input'][key].tolist()
except:
pass
return d
cell=[(0, b, b),
(b, 0, b),
(b, b, 0)])
RWIGS = [1.0, 1.1, 1.25, 1.5, 2.0, 2.5, 3.0, 4.0, 5.0 ]
ED, WD, N = [], [], []
for rwigs in RWIGS:
with jasp('bulk/pd-ados') as calc:
calc.clone('bulk/pd-ados-rwigs-{0}'.format(rwigs))
with jasp('bulk/pd-ados-rwigs-{0}'.format(rwigs)) as calc:
calc.set(rwigs=[rwigs])
try:
calc.calculate()
except (VaspSubmitted, VaspQueued):
continue
# now get results
ados = VaspDos(efermi=calc.get_fermi_level())
energies = ados.energy
dos = ados.site_dos(0, 'd')
#we will select energies in the range of -10, 5
ind = (energies < 5) & (energies > -10)
energies = energies[ind]
dos = dos[ind]
Nstates = np.trapz(dos, energies)
occupied = energies <= 0.0
N_occupied_states = np.trapz(dos[occupied], energies[occupied])
ed = np.trapz(energies * dos, energies) / np.trapz(dos, energies)
wd2 = np.trapz(energies**2 * dos, energies) / np.trapz(dos, energies)
N.append(N_occupied_states)
ED.append(ed)
WD.append(wd2**0.5)
plt.plot(RWIGS, N, 'bo', label='N. occupied states')
def drawPropagation(xmin, xmax, z, doslist):
sy = z.size
#
# temporary read DOSCAR for getting size
#
dos = VaspDos(doscar=doslist[0])
T = dos.energy
idx = np.where((xmin < T) & (T < xmax)) # limit xmin-xmax
T = T[idx]
sx = T.size
T = np.tile(T, (sy, 1)) # extend T
z = np.tile(z, (sx, 1)).T
for i, idoscar in enumerate(doslist):
dos = VaspDos(doscar=idoscar)
efermi = get_efermi_from_doscar(idoscar)
T[i] += efermi
U = dos.dos[idx]
U = np.tile(U, (sy, 1))
for i, idoscar in enumerate(doslist):
dos = VaspDos(doscar=idoscar)
U[i] = dos.dos[idx]
U[i, 0] = 0.0
U[i, -1] = 0.0 # to make bottom line flat
fig = plt.figure(figsize=(12, 12))
ax = fig.add_subplot(1, 1, 1, projection="3d", proj_type="ortho")
verts = []
for i, idoscar in enumerate(doslist):
efermi = get_efermi_from_doscar(idoscar)
verts.append(list(zip(T[i, :] - efermi, U[i, :] / np.max(U[i, :]))))
poly = PolyCollection(verts,
facecolors=(1, 1, 1, 1.0),
edgecolors=(0, 0, 0, 1),
linewidth=1.4) # RGBA
ax.add_collection3d(poly, zs=z[:, 0], zdir="y")
ax.set_xlim3d(xmin, xmax)
ax.set_ylim3d(np.min(z) - 2.0, np.max(z) - 2.0)
ax.set_zlim3d(0, 1.1)
labels = []
for idoscar in range(len(doslist)):
labels.append(doslist[idoscar].split("_")[1])
ax.set_yticks(np.linspace(np.min(z), np.max(z), len(doslist)))
ax.set_yticks(z[:, 0])
ax.set_yticklabels(labels,
va='center',
ha='left',
fontsize=14,
fontname="Arial")
ax.grid(False)
ax.set_xticks(np.arange(xmin, xmax + 1, 2))
ax.set_xticklabels(np.arange(xmin, xmax + 1, 2),
fontsize=14,
fontname="Arial")
ax.set_zticks([])
ax.w_xaxis.set_pane_color((1.0, 1.0, 1.0, 1.0))
ax.w_zaxis.set_pane_color((0.0, 0.0, 0.0, 1.0))
ax.xaxis.pane.set_edgecolor('black')
ax.yaxis.pane.set_edgecolor('black')
ax.xaxis.pane.fill = False
ax.yaxis.pane.fill = False
ax.zaxis.pane.fill = False
ax.get_proj = lambda: np.dot(Axes3D.get_proj(ax),
np.diag([1.0, 5.0, 0.1, 1]))
ax.view_init(elev=15, azim=270)
save(result_file, '3rd calculation \n total energy : {0} eV, {1} eV/atom'.format(p, p/len(atoms)))
save(result_file, 'magnetic moment : {0} mB, {1} mB/atom'.format(m, m/len(atoms)))
save(result_file, 'forces \n {0}'.format(atoms.get_forces()))
calc.set(ismear=-5, lorbit=11, nedos=3001)
p = atoms.get_potential_energy()
save(result_file, '4th calculation \n total energy : {0} eV, {1} eV/atom'.format(p, p/len(atoms)))
tm = atoms.get_magnetic_moment()
m = atoms.get_magnetic_moments()
save(result_file, 'total magnetic moment : {0} mB {1} mB/atom '.format(tm, tm/len(atoms)))
save(result_file, 'magnetic moment: {0}'.format(m))
vdos = VaspDos()
vdos.read_doscar('DOSCAR')
print vdos.efermi
print vdos.site_dos(0,0)
dos = DOS(calc, width=0.05)
d = dos.get_dos()
up = dos.get_dos(0)
down = dos.get_dos(1)
e = dos.get_energies()
plt.plot(e,d, label='total')
plt.plot(e,up, label='spin-up')
from step0 import *
from numpy import *
from ase.dft import DOS
from ase.dft import get_distribution_moment
from ase.calculators.vasp import VaspDos
os.chdir('work-dos')
emax, emin, ngrid, efermi = dos_info('DOSCAR')
vdos = VaspDos()
vdos.read_doscar('DOSCAR')
vdos._set_efermi(efermi)
e = vdos.energy
dos_total = vdos.dos
dos_s = np.zeros(len(e))
dos_p = np.zeros(len(e))
dos_d = np.zeros(len(e))
for i in range(len(atoms)): # atomic type number
dos_s += vdos.site_dos(i,'s')
dos_p += vdos.site_dos(i,'px') + vdos.site_dos(i,'py') + vdos.site_dos(i,'pz')
dos_d += vdos.site_dos(i,'dxy') + vdos.site_dos(i,'dyz') + vdos.site_dos(i,'dz2') + vdos.site_dos(i,'dxz') + vdos.site_dos(i,'dx2')
# dos_s_up = vdos.site_dos(4,'s-up')
# dos_p_up = vdos.site_dos(4,'px-up') + vdos.site_dos(4,'py-up') + vdos.site_dos(4, 'pz-up')
draw_pdos = True
else:
draw_pdos = False
doscar = "DOSCAR_" + system
sigma = 20.0
#
# finding natom
#
f = open(doscar, "r")
line1 = f.readline()
natom = int(line1.split()[0])
f.close()
dos = VaspDos(doscar=doscar)
ene = dos.energy
tdos = dos.dos
tdos = smear_dos(ene, tdos, sigma=sigma)
if draw_pdos:
pdos = np.zeros(len(tdos))
for i in range(0, natom):
pdos = pdos + dos.site_dos(i, orbital)
pdos = smear_dos(ene, pdos, sigma=sigma)
sb.set(context='notebook',
style='darkgrid',
palette='deep',
font='sans-serif',
if len(argvs) == 3:
orbital = argvs[2]
draw_pdos = True
else:
draw_pdos = False
doscar = "DOSCAR_" + system
sigma = 10.0
#
# finding natom
#
f = open(doscar, "r")
line1 = f.readline()
natom = int(line1.split()[0])
f.close()
dos = VaspDos(doscar=doscar)
ene = dos.energy
tdos = dos.dos
tdos = smear_dos(ene, tdos, sigma=sigma)
outname = system + ".txt"
fout = open(outname, "w")
for i, x in enumerate(ene):
fout.write("{0:<12.4f}{1:12.4e}\n".format(ene[i], tdos[i]))
fout.close()
norbs = len(argvs) - 3 # number of orbitals
efermi = get_efermi_from_doscar(doscar)
#
# get orbital list
#
for i in range(0, norbs):
orbitals.append(str(argvs[i + 3]))
#
# finding natom
#
f = open(doscar, "r")
line1 = f.readline()
natom = int(line1.split()[0])
f.close()
dos = VaspDos(doscar=doscar)
ene = dos.energy
tdos = dos.dos
system = obj.system # already know!
lattice = obj.lattice
data = obj.data
#
# limit analysis only for occupied part
#
margin = 0.0
ene = list(filter(lambda x: x <= efermi + margin, ene))
for orbital in orbitals:
#
nargs=2)
parser.add_option("-o",
"--orbital",
action="store",
type="string",
default="all",
help="specify orbitals for which atoms will be printed",
nargs=1)
(options, args) = parser.parse_args()
num = len(sys.argv)
if (num < 2):
parser.print_help()
else:
doscar = VaspDos(sys.argv[num - 1])
# get number of atoms
dos_size = len(doscar._site_dos[0][0])
number_of_atoms = len(doscar._site_dos)
energy = doscar._get_energy()
if (dos_size != len(energy)):
print "Error: The DOS array size (", dos_size, ") is difrent than the energy array size (", len(
energy), ")"
# atoms seting
a = []
if (options.atoms[0] == -1 and options.atoms[1] == -1):
a = [1, number_of_atoms]
else:
